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Wednesday, January 27, 2016

The recent editorial by Drs. Longo and Drazen in the New England Journal of Medicine (NEJM) [1] has stirred up quite a bit of controversy. As Executive Officers of the International Society of Computational Biology, Inc. (ISCB), we express our deep concern about the restrictive and potentially damaging opinions voiced in this editorial. While some of the concerns voiced by the authors of the editorial are worth considering, large parts of the statement purport an obsolete view of hegemony over data that is neither in line with today's spirit of open access nor furthering an atmosphere where the potential of data can be fully realized.

We acknowledge that the additional comment on the editorial [2] eases some of the polemics, unfortunately without addressing some of the core issues. We still feel, however, that we need to contrast the opinion voiced in the editorial with what we consider the axioms of our scientific society, statements that lead into a fruitful future of data-driven science:

• Data produced with public money should be public in benefit of the science and society
• Restrictions to the use of public data hamper science and slow progress
• Open data is the best way to combat fraud and misinterpretations

Current large data collections proceed from many sources are continually accumulated and require a variety of analytical approaches. Data generation and data analysis overlap in time and are continually updated with new data sets produced by new techniques and new analysis methodologies. Furthermore, in many cases current science functions in consortia in which scientists collaborate toward common goals while preserving their own scientific objectives. Dividing scientists into data providers and data analysts is simplistic and gives a misleading impression of the actual state of biological and biomedical science.

We very much support collaboration between disciplines, including experimental and clinical as well as bioinformatics, as the best way forward to address complex biological problems. But this collaboration cannot be based on imposed restrictions to data access and cannot be contained in professional silos. (The use of expressions such as "research parasites" clearly does not help.)

Many bio-communities have made significant progress by endorsing open data policies and, gratefully, public funding agencies have connected to the spirit that they are distributing taxpayers' money to science and that, therefore, the data that are generated in the course belong to the public. It is, perhaps, natural that some areas of biomedical research are slow in adopting these policies. History and the confidential nature of the relevant data are surely one of the reasons. However, in our opinion data hegemony is another, a reason that has to be overcome. The sooner these barriers to progress are removed the sooner the patients will benefit from the current flourishing of biomedical research.

Friday, January 22, 2016

The American Institute for Medical and Biological Engineering (AIMBE) has announced the pending induction of Bonnie Berger, Ph.D., Professor of Applied Math and Computer Science at MIT, and head of the Computation and Biology group,, Massachusetts Institute of Technology, to its College of Fellows. Dr. Berger was nominated, reviewed, and elected by peers and members of the College of Fellows for outstanding research contributions to computational biology and mentoring of future bioinformatics leaders.

The College of Fellows is comprised of the top two percent of medical and biological engineers in the country. The most accomplished and distinguished engineering and medical school chairs, research directors, professors, innovators, and successful entrepreneurs, comprise the College of Fellows.

AIMBE Fellows are regularly recognized for their contributions in teaching, research, and innovation. AIMBE Fellows have been awarded the Presidential Medal of Science and the Presidential Medal of Technology and Innovation and many also are members of the National Academy of Engineering, National Academy of Medicine, and the National Academy of Sciences.

A formal induction ceremony will be held during AIMBE's 25th Annual Meeting at the National Academy of Sciences Great Hall in Washington, DC on April 4, 2016. Dr. Berger will be inducted along with 160 colleagues who make up the AIMBE College of Fellows Class of 2016. For more information about the AIMBE Annual Meet, please visit www.aimbe.org.

AIMBE's mission is to recognize excellence in, and advocate for, the fields of medical and biological engineering in order to advance society. Since 1991, AIMBE's College of Fellows has lead the way for technological growth and advancement in the fields of medical and biological engineering. Fellows have helped revolutionize medicine and related fields in order to enhance and extend the lives of people all over the world. They have also successfully advocated for public policies that have enabled researchers and business-makers to further the interests of engineers, teachers, scientists, clinical practitioners, and ultimately, patients.

For questions regarding the College of Fellows and AIMBE, please contact Jason R. Hibner, AIMBE Director of Member Services and Operations at jhibner@aimbe.org, or call the AIMBE office at 202-496-9660.

American Institute for Medical and Biological Engineering: www.aimbe.org
Providing Leadership & Advocacy for Medical and Biological Engineering for the Benefit of Society

We would like to ask you 10 questions to assess your needs for a registry of standards in the life, environmental, and biomedical sciences.

If widely used, community-driven standards can help scientists to broadly represent, annotate and share digital information in ways that enable their re-use, reproducibility and further exploration. Did you know there are >600 standards in the life, environmental and biomedical sciences? We know that many researchers, developers, curators, funders, journal editors, and librarians lack the support and guidance on how to best select standards and understand their maturity, or to find tools and databases that implement them.

BioSharing is a curated, web-based, searchable portal of standards. Since 2011, Biosharing has ensured standards are registered and discoverable, and has monitored their maturity and evolution, and in doing so has helped provide enough information for our growing user base to make informed decisions. This is your time to drive enhancements to BioSharing, under several research and infrastructure programmes. Your feedback will:
Provide a review of BioSharing content and functionality as the ELIXIR Standards Registry, under the EuropeanELIXIR EXCELERATE project
Define BioSharing activities under the US NIH Big Data to Knowledge (BD2K ) initiative, specifically to:
Work with the NIH Associate Director for Data Science (ADDS ) office to ensure BioSharing is formally embedded in the complementary activities of the BD2K Standards Coordinating Centre
Inform the contribution to the selection and usage of standards in the BD2K Data Discovery Index (bioCADDIE ) project, and the Centre for Expanded Data Annotation and Retrieval (CEDAR )
Contribute to the BioSharing Working Group, operating jointly under the Force 11/Research Data Alliance (RDA)working groups .

Once again, I am preparing an annual review of progress in translational bioinformatics, and am seeking nominations for exciting papers published between January 2015 and the present. The talk will be on March 21 in San Francisco as part of https://www.amia.org/jointsummits2016

This talk is now in its 9th year and I hope is a useful way to highlight great work in our field.

To remind you, I am looking for papers that relate clinical entities (patients, diseases, drugs, symptoms, signs, populations) to molecular entities (genes, molecules, RNA, proteins) using informatics technologies. Self-nominations are welcome, and nominations of the papers of others are even better.

You can send me the paper, the citation, PMID, or whatever. If you want to tell me why you nominate a paper, great, but you don\\\'t have to--I will read the papers and try to form an opinion. The previous talks are available at: https://rbaltman.wordpress.com

Thanks so much for your help. I try to acknowledge all contributors in the the talk (let me know if you prefer to be anonymous). Please forward this message to colleagues who may have thoughts.